fastadir=$1
fastaname=$2
tempdir=$3
outputdir=$4
treenameprefix=$5
memforinputbuffers=300000000
maxsubtree=$6

./fastatotext $fastadir $fastaname $tempdir $treenameprefix $outputdir 0 10000 1000000
./texttodna $tempdir $treenameprefix $outputdir $treenameprefix 1
./encodeFolder $outputdir $treenameprefix $tempdir $treenameprefix
./sortPartitions $outputdir $tempdir $treenameprefix
./mergeToSuffixTree $tempdir $outputdir $treenameprefix $memforinputbuffers $maxsubtree



